Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Microarray analysis of exogenous NAD+-induced transcriptome changes in Arabidopsis thaliana

ABSTRACT: The goal of the microarray was to investigate the transcriptome changes induced by exogenous NAD+ in the wild-type Col-0 plants. Results showed that exogenous NAD+-induced dramatic transcriptional changes in Arabidopsis. Particularly, a large group of salicylic acid pathway genes including NPR1 and its traget genes were induced by NAD+, whereas the jasmonic acid/ethylene pathway defense marker gene PDF1.2 was inhibited by NAD+ treatment. In addition, a group of the pathogen-associated molecular pattern pathway genes were also induced by exogenous NAD+. These results indicate that exogenous NAD+ induces defense pathways against (hemi)biotrophic pathogens but suppresses defense against necrotrophs. Two to three replicates with leaves from 8-12 plants per sample were collected at 0, 4, and 24 hr after NAD+ treatment. Leaf tissues were collected as the control at 0 hr, and NAD+-treated leaf tissues were collected at 4 and 24 hr. After extraction, RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Equal amount of RNA from the biological replicates were used for microarray analysis.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Zhonglin Mou

PROVIDER: E-GEOD-76568 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Plants growth and development is highly dependent on the environment. During there lifespan, plants are submitted to changing environmental conditions that requires constant metabolic adjustments. In particular, in vitro cultured plantlets are exposed, throughout micropropagation, to unique growth conditions characterized by distinctive levels of nitrogen, exogenous sugar, light and atmospheric conditions. To resume growth upon transfer ex vitro, in vitro plantlets must acclimatize to natural conditions. In this study, the impact of the in vitro environment on the expression profile of tomato (Solanum Lycopersicum) plantlets was analysed using the microarray and real-time PCR methods. After 20 days of growth in vitro, a significant increase in expression of genes linked to photosynthesis, nitrogen metabolism and salicylic acid signaling pathways was observed. By opposition, the expression of transcripts associated to carbohydrate metabolism and jasmonic acid signaling pathway were reduced. Also, the expression of reactive oxygen scavenging (ROS) enzymes in the mitochondrias, chloroplasts and cytosol were altered in in vitro cultured tomato plantlets. More precisely, the in vitro environment led to increased photosynthetic gene expression, lower sink strength, up-regulation of nitrogen assimilation and induced a specific stress response in tomato plantlets. Our results suggest that the presence of exogenous sugar is an important environmental cue that governs the modified cell ROS pattern, defense-related genes modulation and abnormal physiology of in vitro plantlets. Keywords: environmental challenge, growth condition comparison, expression profile Three biological replicates consisting of three individual plantlets grown in different vessels (in vitro) or pots (ex vitro) were used for the competitive hybridization. To reduce possible bias due to the difference in the properties of both dyes, two technical replicates consisting of dye swap were realized. The complete experiment required six microarrays.

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Microarray analysis of exogenous NAD+-induced transcriptome changes in Arabidopsis thaliana

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